title: Brain of adult C57Bl6j mouse_tail-suspended hindlimb-unloaded_rep4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Effect of microgravity on brain gene expression in mice

hyb_protocol: We used brains of four control (C1, C2, C3, C4) and four tail-suspended hindlimb-unloaded (E1, E2, E3, E4) mice to ensure statistical relevance of the study. 60 ug of total RNA extracted in TRIzol from each brain was reversed transcribed into labeled cDNAs using fluorescent Cy5 or Cy3-dUTP (Amersham Biosciences, NJ). Differently labeled cDNAs obtained from a pair of biological replicas were co-hybridized overnight at 50C with a microscope slide spotted with ~ 27,000 mouse cDNA sequences produced by the Microarray Core Facility of the Albert Einstein College of Medicine in the “multiple yellow” design (i.e.: C1C2, C3C4, E1E2, E3E4), described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38).

scan_protocol: Slides were scanned with GenePix 4000A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 3.0.6.90 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in house developed algorithms described in Iacobas DA, Iacobas S, Li WEI, et al. Physiol Genomics 20: 211-223, 2005.

source_name: Brain of tail-suspended hindlimb-unloaded adult C57Bl6j mouse

label_protocol: 60 ug of total RNA extracted in TRIzol from each brain was reversed transcribed into labeled cDNAs using fluorescent Cy3-dUTP (Amersham Biosciences, NJ)

growth_protocol: All animals sacrificed within 1 hour in the morning to avoid differences in the circadian and homeostatic sleep-wake factors. The brains were immediately removed and placed in liquid nitrogen.

extract_protocol: TRIzol (Invitrogen, CA)

treatment_protocol: hindlimb-unloaded

tag: strain

value: C57Bl6J, gender:male, age:5-6 months, treatment:hindlimb-unloaded, tissue:brain


title: Follicular lymphoma, diagnostic biopsy: 46229

status: Public on Aug 09 2008

type: genomic

city: Vancouver

first: K-John

last: Cheung

state: BC

address: 600 West 10th Ave

country: Canada

institute: British Columbia Cancer Agency

description: Follicular lymphoma, diagnostic biopsy

hyb_protocol: Probe pre-hybridization Denature the probe at 85ºC for 10 minutes Allow the Cot-1 DNA to anneal to the DNA probe for 1 hour at 45ºC. Hybridization Maintain the probe at 45ºC. (If necessary pulse-spin the tube to pool any condensed probe.) Pipet 43 ul of the probe solution onto a 24 x 60 mm coverslip prewarmed to 45ºC. Gently lower the slide over the coverslip (try to avoid generating bubbles). Place the slide into a hybridisation cassette. Add 10 ul water into the lower groove of the cassette. Close the hybridization cassette ensuring a good seal is made by the gasket. Incubate for 36-40 hours at 45ºC. Washing Prewarm the wash buffer (0.1 xSSC with 0.1% SDS) to 45ºC. Remove the slide from the hybridization cassette. Soak slide in wash buffer until the coverslip slides off (usually 2-5 minutes). Transfer slide immediately into a fresh coplin jar containing wash buffer. Wash the slide in wash buffer for 5 minutes with agitation. Quickly change the wash buffer and repeat the wash step another 2 times. Rinse the slide with 3 changes of 0.1 x SSC at room temperature, leaving the slide in the final 0.1x SSC so it will not dry out. Dry the slide with a filtered air stream, or centrifuge the slide in a clean, dust-free 50 ml Falcon tube at 700 g for 3 minutes. Store the slides in a dark, dust free box until ready to scan. (If the slides are not scanned within 2 hours, vacuum seal the slide box and leave the box at room temperature until scanning will take place.

scan_protocol: Images were scanned using and API Arrayworx e Auto Scanner. Data was processed using the Softworx (API) analysis package. An Applied Precision Arrayworx CCD scanner is used to scan slides at a 9.75 um resolution and at a high signal to noise ratio (SNR). The exposure time for each image wavelength is between 0.2-2 seconds, the standard exposure time is 1.00 sec for Cy3 and 2.00 sec for Cy5.

data_processing: Data was normalized using the application described in Khojasteh et al BMC Bioinformatics 2005;6:274

label: Cyanine 5

molecule: genomic DNA

organism: Homo sapiens

source_name: Follicular lymphoma, diagnostic biopsy

label_protocol: cy3/cy5 labeling

extract_protocol: Genomic DNA extracted by standard ProtK extraction.

tag: tumor grade

value: Tumor grade 2

tag: Overall survival from diagnosis (year)

tag: Time to transformation from diagnosis (year)

label: Cyanine 3

source_name: Normal genomic

tag: Novagen female Genomic DNA


title: F.candida_Cadmium_Day7_02

status: Public on Aug 08 2008

type: RNA

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: No additional information available.

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 4 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma (2.9.1) package in the R (2.4.0) software environment (http://www.R-project.org/), which consisted of Edward’s background correction (set off = 30) and global loess normalization. For each channel the median background intensity was substracted from the mean signal (foreground) intensity.

molecule: total RNA

organism: Folsomia candida

source_name: F.candida, Cadmium, 7 days

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 30 days old, exposed for 7 days in a jar containing LUFA 2.2 soil spiked with cadmium (57.9 ug/g (DW)).

source_name: F.candida, Reference, 7 days

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 30 days old, exposed for 7 days in a jar containing control (reference) LUFA 2.2 soil (non-spiked).


title: TNC deficient mouse muscle Null C15 201

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

description: see other fields

hyb_protocol: Annealing: 16h @ 68°C in ExpressHyb (Clontech Laboratories, Inc., Ozyme, FRANCE). Washing: 4x in (2xSSC, 1% SDS) @68°C for 1h. 1x in (0.1xSSC, 0.5% SDS) @68°C for ½ h, 1x in (2x SSC) @room temperature for 5min.

scan_protocol: Exposure: Phosphoimager screen, 4-10 daysHard & Software: Phosphorimager #425E and ImageQuant v. 3.3 (Molecular Dynamics, Sunnyvale, California, USA). Image analysis: For each spot, the pixel sum was determined with AIDA software (Raytest Schweiz AG, Urdorf, Switzerland). Background was determined from the mean of empty areas on predefined areas of the filter

data_processing: Signals were background corrected and normalized to the signal of all mRNAs on the filter  (all signals except 18S rRNA and 28S rRNA)

organism: Mus musculus

source_name: Soleus muscle

label_protocol: Target labeling: reverse transcription of 4 microg total RNA with gene specific primers @50°C using Superscript RT (Life Technologies AG, Basel, SWITZERLAND), [alpha-32P]dATP, and  S-modified dCTP (Ambion (Europe) Ltd, Cambridgeshire, UK).

extract_protocol: RNA extraction: From cryosections from the belly portion of the muscle wit RNeasy mini kit (Qiagen AG, SWITZERLAND).

treatment_protocol: Soleus Muscle of cage controls

tag: 129/SV mice


title: Brain of adult C57Bl6j mouse_tail-suspended hindlimb-unloaded_rep3

state: TX

country: USA

label_protocol: 60 ug of total RNA extracted in TRIzol from each brain was reversed transcribed into labeled cDNAs using fluorescent Cy5-dUTP (Amersham Biosciences, NJ)


title: Brain of adult C57Bl6j mouse_tail-suspended hindlimb-unloaded_rep1


title: Brain of adult C57Bl6j mouse_control_rep3

source_name: Brain of control adult C57Bl6j mouse

treatment_protocol: control mice (no treatment)

value: C57Bl6J, gender:male, age:5-6 months, treatment:control , tissue:brain


title: Brain of adult C57Bl6j mouse_tail-suspended hindlimb-unloaded_rep2


title: Brain of adult C57Bl6j mouse_control_rep4


title: F.candida_Cadmium_Day4_03

description: No additional information available.

source_name: F.candida, Reference, 4 days

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 27 days old, exposed for 4 days in a jar containing control (reference) LUFA 2.2 soil (non-spiked).

source_name: F.candida, Cadmium, 4 days

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 27 days old, exposed for 4 days in a jar containing LUFA 2.2 soil spiked with cadmium (57.9 ug/g (DW)).


title: F.candida_Cadmium_Day7_01

description: No additional information available.


title: F.candida_Cadmium_Day4_04

description: No additional information available.


title: Reloading of mouse muscle WT R1 203

description: see other fields

treatment_protocol: Muscle after 1 day of reloading subsequent to 7 days of Hindlimb suspension


title: Reloading of mouse muscle WT R1 202

description: see other fields


title: Reloading of mouse muscle WT R1 175

description: see other fields


title: F.candida_Cadmium_Day2_04

description: No additional information available.

source_name: F.candida, Reference, 2 days

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing control (reference) LUFA 2.2 soil (non-spiked).

source_name: F.candida, Cadmium, 2 days

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with cadmium (57.9 ug/g (DW)).


title: espR knockout (deltaR) rep2

city: San Francisco

first: Paolo

last: Manzanillo

state: CA

department: Microbiology and Immunology

institute: University of California at San Francisco

description:
Biological replicate 2
espR knockout (deltaR rep2)

hyb_protocol: Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h. After hybridization, slides were washed in batch.

scan_protocol: Slides were scanned using an Axon 4000B scanner and GenePix software. Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software.

data_processing: Ratio-based normalization using Acuity 4.0, followed by a dye-swap using the Acuity program so that the processed data would reflect (Cy5-M.tb strain RNA/Cy3-Reference Pool RNA).

organism: Mycobacterium tuberculosis

source_name: espR knockout M.tb

label_protocol: 5 ug total RNA was reverse transcribed into cDNA using random hexamer primers in the presence of aa-dUTP. cDNA was labelled with Cy dyes (Amersham) and purified over Zymo DNA binding columns.

growth_protocol: M. tuberculosis growing in 7H9 with 0.05% Tween 80 in early log phase.

extract_protocol: RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA was purified with Qiagen Rneasy columns per manufacturers instructions.

tag: M. tuberculosis Erdman strain

source_name: Reference Pool

tag: Pooled from all samples used


title: F.candida_Cadmium_Day4_01

description: No additional information available.


title: Brain of adult C57Bl6j mouse_control_rep2


title: Reloading of mouse muscle WT R1 177

description: see other fields


title: Brain of adult C57Bl6j mouse_control_rep1


title: F.candida_Cadmium_Day2_03

description: No additional information available.


title: Wt rep2

description:
Biological replicate 2
Wild type M.tb (WT rep2)

source_name: WT M.tb


title: Reloading of mouse muscle WT R1 178

description: see other fields


title: mouse muscle WT C16 197

description: see other fields

treatment_protocol: Soleus Muscle of cage control mice


title: F.candida_Cadmium_Day4_02

description: No additional information available.


title: Reloading of mouse muscle WT R1 176

description: see other fields


title: F.candida_Cadmium_Day2_02

description: No additional information available.


title: F.candida_Cadmium_Day2_01

description: No additional information available.


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 4 Tech Replicate 1

city: Mobile

first: Jonathon

last: Audia

state: AL

address: 307 University Blvd N

institute: University of South Alabama

description: These data are the first global analysis of the R. prowazekii transcriptome and provide insight into the mechanisms employed by rickettsiae to adapt to temperature upshifts.

hyb_protocol: All components were cleaned using an air gun canister prior to assembly of the microarray hybridization chamber/ microarray/ coverslip apparatus.  Hybridization and washing were performed as follows: 1) Add 100ul of 4xSSC to the humidity well in each hybridization chamber. 2) Heat cDNA probes (20 ul) for 10 minutes at 80 C and apply to the glass slides followed by application of coverglass and clamps. 3) Incubate hybridization chamber overnight at 42 C. 4) Remove slides from chamber and wash in 2x SSC, 0.2% SDS (in MilliQ water) with agitation for 12 minutes at ambient temperature. 5) Wash in 2x SSC with agitation for 12 minutes at ambient temperature. 6) Wash in 0.2x SSC with agitation for 12 minutes at ambient temperature. 7) Remove slides and spin in microcentrifuge for 30 secs. 8) Apply Genisphere 3DNA capture reagents as per the manufacturer’s directions. 9) Wash slides as described in steps 4 – 6.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0.

data_processing: Slides were scanned and the resulting values were background subtracted.  Data was imported into GeneSpring 7.1 and normalized by a Lowess curve is fit to the log-intensity versus log-ratio plot. 20.0% of the data is used to calculate the Lowess fit at each point. This curve is used to adjust the control value for each measurement. If the control channel is lower than 10 RFU then 10 is used instead.  The Heat Shock induction ratio (VALUE column) was calculated by dividing the fluorescence intensity of each spot in the Heat Shock (42 C) sample by that of the corresponding Control (34 C) sample.

organism: Rickettsia prowazekii str. Madrid E

source_name: Heat Shock (42 C, 30 minutes)

label_protocol: Purified rickettsial RNA (2 ug) was converted cDNA using random hexamers and labeled using the 3DNA Array 900MPX Detection system from Genisphere.  The Genisphere detection system employs indirect labeling using fluorescent dendrimers subsequent to cDNA synthesis.

extract_protocol:
Rickettsiae were released from Lcells by ballistic shearing using a Mini-BeadbeaterTM (BioSpec Products, OK) to deliver a 5 sec pulse followed by incubation on ice for 20 sec (repeated three times).  The lysate was removed and the beads were washed 3 times with SPGMg-Sierra (sucrose, 0.281 M; KH2PO4, 3.76 mM; K2HPO4, 7.1 mM; glutamic acid, 5 mM; MgCl2, 10 mM; pH 7.0 containing 20 % (v/v) Sierra DNA/RNA Protect from Sierra Diagnostics) resulting in approximately 4 ml of lysate.  L-cell debris was removed by low speed centrifugation (5 min, 1,150 x g, 24 oC), the supernatant transferred to a 30 ml Corex tube, and rickettsiae collected by centrifugation (15 min, 9,600 x g, 4 oC).  The supernatant was removed and 0.1 ml of SPGMg-Sierra was added to the rickettsial pellet which was mulled with a pestle.  A 1 ml volume of RNA Wiz (Ambion) was added and the suspension vortexed vigorously.  Total RNA was extracted as per the manufacturer’s directions but in lieu of the final precipitation step, a 0.56 volume of 100 % ethanol was added slowly with thorough mixing prior to application onto a Qiagen RNeasy mini spin column.  Following an on-column DNaseI (Qiagen) digestion step (as per the manufacturer’s directions), total RNA was eluted from the column twice (final volume of 60 ul) in RNase-free water containing 0.1 mM EDTA (pH 8.0).  Total RNA (L-cell and rickettsial) quality and quantity were determined using an Agilent Bioanalyzer.
Contaminating host RNA was removed from the preparation prior to microarray analyses using Ambion’s MICROBEnrich technology as per the manufacturer’s directions, resulting in the removal of ~90 % of the host RNA.

tag: Rickettsia prowazekii Madrid E grown in L929 mouse fibroblast cells for 48 hrs (initial infection of 1-10 rickettsiae/Lcell and ~200-300 rickettsiae/Lcell at harvest) were shifted to 42 C for 30 minutes and total rickettsial RNA purified away from host RNA.

source_name: Control (34 C)

tag: Rickettsia prowazekii Madrid E grown in L929 mouse fibroblast cells for 48 hrs (initial infection of 1-10 rickettsiae/Lcell and ~200-300 rickettsiae/Lcell at harvest) at 34 C and total rickettsial RNA purified away from host RNA.


title: espR transposon mutant (R-) rep1

description:
Biological replicate 1
espR transposon mutant (R- rep1)

source_name: espR transposon mutant M.tb


title: espR knockout (deltaR) rep1

description:
Biological replicate 1
espR knockout (deltaR rep1)


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 4 Tech Replicate 2


title: mouse muscle WT C15 205

description: see other fields

treatment_protocol: Soleus muscle of cage control mice


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 3 Tech Replicate 2


title: espR transposon mutant (R-) rep2

description:
Biological replicate 2
espR transposon mutant (R- rep2)


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 2 Tech Replicate 2


title: Wt rep1

description:
Biological replicate 1
Wild type M.tb (WT rep1)


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 3 Tech Replicate 1


title: mouse muscle WT C15 185

description: see other fields


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 2 Tech Replicate 1


title: mouse muscle WT C15 186

description: see other fields


title: mouse muscle WT C15 204

description: see other fields


title: mouse muscle WT C15 184

description: see other fields


title: Reloading of TNC deficient mouse muscle Null R1 199

description: see other fields

treatment_protocol: Soleus Muscle of 1 day reloaded mice

tag: Tenascin-C deficient 129/SV mice


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 1 Tech Replicate 2


title: mouse muscle WT C15 183

description: see other fields


title: espR mutant complemented with WT espR (R+) rep2

description:
Biological replicate 2
espR mutant complemented with WT espR (R+ rep2)

data_processing: Ratio-based normalization using Acuity 4.0.

source_name: espR mutant M.tb complemented with wild type espR gene


title: espR mutant complemented with N-terminal Flag espR (RFL) rep2

description:
Biological replicate 2
espR mutant complemented with N terminal Flag espR (RFL rep2)

source_name: espR mutant M.tb complemented with Flag-espR gene


title: WT rep2


title: espR mutant (R-) rep2

description:
Biological replicate 2
espR mutant (R- rep2)

source_name: espR mutant M.tb


title: Reloading of TNC deficient mouse muscle Null R1 198

description: see other fields


title: Reloading of TNC deficient mouse muscle Null R1 180

description: see other fields


title: Reloading of TNC deficient mouse muscle Null R1 179

description: see other fields


title: Reloading of TNC deficient mouse muscle Null R1 182

description: see other fields


title: Reloading of TNC deficient mouse muscle Null R1 181

description: see other fields


title: Rickettsia prowazekii Control vs Heat Shock Biological Replicate 1 Tech Replicate 1


title: TNC deficient mouse muscle Null C15 200

description: see other fields


title: TNC deficient mouse muscle Null C15 195

description: see other fields


title: Sample 2rev vancomycin treated subinhibitory conc.

city: Padua

first: Roberta

last: Provvedi

address: Via Gabelli 63

department: Biologia

country: Italy

institute: University of Padua

description: no additional information

hyb_protocol: Combine labeled sample with 10 mg/ml tRNA, 20X SSC, Formamide, % SDS. Full details at www.cag.icph.org

scan_protocol: After hybridization slides were immediately scanned using a 428TMArray Scanner (Affymetrix). Fluorescence intensities of Cy3 and Cy5 dyes at each spot were quantified using the ImaGene software 4.1 (BioDiscovery, Inc.)

data_processing:
Data obtained from qualified spots were normalized using the print-tip LOESS with a web-based tool for Diagnosis and Normalization of spotted cDNA MicroArrayData (DNMAD) available at http://dnmad.bioinfo.cnio.es
Values are expressed as ratio Cy3/Cy5 spot's intensity determined from the normalized fluorescence intensity.

source_name: H37Rv vancomycin treated culture

label_protocol: Combine total RNA, random primers and reaction mix (5X First-Strand buffer, 100 mM DTT, dTdNTP mix, Cy3 or Cy5). Full details at www.cag.icph.org.

growth_protocol: Culture grown to mid-log phase in Middlebrook 7H9 supplemented with ADC and 5 ug/ml of vancomycin

extract_protocol: Bacteria were thawed on ice and added to prechilled 15 ml screw-capped polypropylene centrifuge tubes containing 1 ml of zirconia/silica beads (0.1 mm diameter, Biospec Products) and 1 ml of phenol-chloroform-isoamyl alcohol (25:24:1). Full details at Manganelli et al. Mol Microbiol (1999) 31:715-724

treatment_protocol: M. tuberculosis H37Rv grown in the presence of 5 ug/ml of vancomycin

tag: Mycobacterium tuberculosis H37Rv strain vancomycin treated

source_name: H37Rv untreated culture

label_protocol: see channel 1

extract_protocol: see channel 1

treatment_protocol: M. tuberculosis H37Rv grown in physiological conditions to exponential phase

tag: Mycobacterium tuberculosis H37Rv strain untreated


title: Sample 2rev vancomycin treated 10XMIC 4 hrs

description: no additional information

growth_protocol: Culture grown to mid-log phase in Middlebrook 7H9 supplemented with ADC

treatment_protocol: M. tuberculosis H37Rv grown in physiological conditions to exponential phase and then incubated for 4 hrs with 400 ug/ml of vancomycin


title: Sample 1rev vancomycin treated 10XMIC 4 hrs

description: no additional information


title: Sample 1rev vancomycin treated subinhibitory conc.

description: no additional information


title: TNC deficient mouse muscle Null C15 191

description: see other fields

source_name: Soleus muscle


title: Sample 1 vancomycin treated subinhibitory conc.

description: no additional information

data_processing:
Data obtained from qualified spots were normalized using the print-tip LOESS with a web-based tool for Diagnosis and Normalization of spotted cDNA MicroArrayData (DNMAD) available at http://dnmad.bioinfo.cnio.es
Values are expressed as ratio Cy5/Cy3 spot's intensity determined from the normalized fluorescence intensity.


title: TNC deficient mouse muscle Null C16-190

description: see other fields


title: TNC deficient mouse muscle Null C15 193

description: see other fields


title: espR mutant complemented with N-terminal Flag espR (RFL) rep1

description:
Biological replicate 1
espR mutant complemented with N terminal Flag espR (RFL rep1)


title: Sample 2 vancomycin treated subinhibitory conc.

description: no additional information


title: Sample 2 vancomycin treated 10XMIC 1 hr

description: no additional information

treatment_protocol: M. tuberculosis H37Rv grown in physiological conditions to exponential phase and then incubated for 1 hr with 400 ug/ml of vancomycin


title: Sample 1 vancomycin treated 10XMIC 4 hrs

description: no additional information


title: TNC deficient mouse muscle Null C15 187

description: see other fields


title: Sample 2 vancomycin treated 10XMIC 4 hrs

description: no additional information


title: Sample 1 vancomycin treated 10XMIC 1 hr

description: no additional information

data_processing: Values are expressed as ratio Cy5/Cy3 spot's intensity determined from the normalized fluorescence intensity.

source_name: Mycobacterium tuberculosis H37Rv culture untreated

tag: Strain H37Rv

tag: Strain H37Rv vancomycin treated


title: Sample 2rev vancomycin treated 10XMIC 1 hr

description: no additional information

tag: Mycobacterium  tuberculosis H37Rv strain untreated


title: Sample 1rev vancomycin treated 10XMIC 1 hr

description: no additional information

tag: Mycobacteriun tuberculosis H37Rv strain vancomycin treated

tag: M. tuberculosis H37Rv untreated


title: Vibrio vulnificus CMCP6 growing in TSBS (biological replicate)

status: Public on Aug 07 2008

city: Portland

first: Jorge

middle: H

last: Crosa

state: OR

address: 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health and Science University

description: Each target is represented on the array by fourteen 24-mer oligonucleotide pairs/ gene. Each pair consists of a sequence perfectly matched (PM) to the ORF and another adjacent sequence with two mismatched (MM) bases was used for background and cross-hybridization determination. Each probe is replicated 3 times. These pairs are synthesized on the chip using the Maskless Array Synthesizer developed by NimbleGenTM. These chips containing the entire V. vulnificus CMCP6 genome were used in the hybridization experiments with the synthesized cRNA.

hyb_protocol: It was performed by Nimblegen. Please refer to www.nimblegen.com

scan_protocol: Microarrays were scanned with an Axon Genepix 4000B scanner at 532 nm and a resolution of 5 µm.

data_processing: The data obtained has been further processed using some tools available through the Bioconductor project (http://www.bioconductor.org) using a quantile normalization and gene calls generated using the RMA algorithm that are based on log2. The values were reverted to decimal scale. The average of the three replicates were subsequently analyzed with GeneSpring 7.0 (Agilent Technologies, Palo Alto, CA) to identify differential gene expression in experimental and control samples. Genes with more than two fold difference of expression between each condition (TSBS vs TSBS + EDDA or TSBS + FAC vs TSBS + EDDA) and a P value <0.01 were further analyzed and described in this manuscript.

label: Biotin

organism: Vibrio vulnificus CMCP6

source_name: Vibrio vulnificus CMCP6 growing in TSBS

label_protocol: The primer employed for cDNA first strand synthesis incorporates a 5’ T7 promoter sequence that was used to synthesize biotinylated cRNA from the ds-cDNA using the Megascript T7 kit (Ambion®, Austin, TX). Following quantification, the cRNA was fragmented with metals and heat, and was hybridized to the V. vulnificus CMCP6 NimbleGenTM array.

extract_protocol: Strains were grown to an OD600nm of 0.6 to 0.8 in TSBS, TSBS with the addition of 250 μg/ml FAC or TSBS with the addition of 50 μM EDDA. Three independent cultures of the V. vulnificus cells grown in each media, were combined and treated as a single sample for the RNA extraction to minimize culture variation. Two samples per condition were used for the microarray analysis. Cells were centrifuged and the pellets resuspended in RNAWiz reagent (Ambion®, Austin, TX). Total RNA was extracted from each strain according to the manufacturer’s instructions, the quality of the RNA was assessed on an Agilent Bioanalyzer 2100 electrophoretic system and 20 µg were used in the synthesis of double-stranded cDNA.

tag: The RNA samples were extracted from Vibrio vulnificus CMCP6 wild type growing in TSBS


title: Vibrio vulnificus CMCP6 growing in TSBS + ferric ammonium citrate (250 ug/ml)

description: Each target is represented on the array by fourteen 24-mer oligonucleotide pairs/ gene.  Each pair consists of a sequence perfectly matched (PM) to the ORF and another adjacent sequence with two mismatched (MM) bases was used for background and cross-hybridization determination.  Each probe is replicated 3 times.  These pairs are synthesized on the chip using the Maskless Array Synthesizer developed by NimbleGenTM.  These chips containing the entire V. vulnificus CMCP6 genome were used in the hybridization experiments with the synthesized cRNA.

data_processing: The data obtained has been further processed using some tools available through the Bioconductor project (http://www.bioconductor.org) using a quantile normalization and gene calls generated using the RMA algorithm that are based on log2.  The values were reverted to decimal scale. The average of the three replicates were subsequently analyzed with GeneSpring 7.0 (Agilent Technologies, Palo Alto, CA) to identify differential gene expression in experimental and control samples.  Genes with more than two fold difference of expression between each condition (TSBS vs TSBS + EDDA  or TSBS + FAC vs TSBS + EDDA) and a P value <0.01 were further analyzed and described in this manuscript.

label_protocol: The primer employed for cDNA first strand synthesis incorporates a 5’ T7 promoter sequence that was used to synthesize biotinylated cRNA from the ds-cDNA using the Megascript T7 kit (Ambion®, Austin, TX).  Following quantification, the cRNA was fragmented with metals and heat, and was hybridized to the V. vulnificus CMCP6 NimbleGenTM array.

extract_protocol: Strains were grown to an OD600nm of 0.6 to 0.8 in TSBS, TSBS with the addition of 250 μg/ml FAC or TSBS with the addition of 50 μM EDDA.  Three independent cultures of the V. vulnificus cells grown in each media, were combined and treated as a single sample for the RNA extraction to minimize culture variation.  Two samples per condition were used for the microarray analysis.  Cells were centrifuged and the pellets resuspended in RNAWiz reagent (Ambion®, Austin, TX).  Total RNA was extracted from each strain according to the manufacturer’s instructions, the quality of the RNA was assessed on an Agilent Bioanalyzer 2100 electrophoretic system and 20 µg were used in the synthesis of double-stranded cDNA.


title: Vibrio vulnificus CMCP6 growing in TSBS

tag: V. vulnificus CMCP6 wild type growing in TSBS


title: Vibrio vulnificus CMCP6 growing in TSBS + ferric ammonium citrate (250 ug/ml) (biological replicate)


title: Vibrio vulnificus CMCP6 growing in TSBS + EDDA (50uM) (biological replicate)

tag: The RNA samples were extracted from Vibrio vulnificus CMCP6 wild type growing in TSBS + EDDA 50uM


title: Vibrio vulnificus CMCP6 growing in TSBS + EDDA 50 uM


title: Motorneuron_SMA_sample3

status: Public on Aug 06 2008

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

institute: University of Milan

description: veichle-treated SMA mouse motoneurons

hyb_protocol: Following fragmentation, 15 micrograms of duoble-amplified cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip Mouse Genome 430A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: veichle-treated SMA mouse motoneurons

label_protocol: Biotinylated cRNA were prepared through a double amplification procedure according to the protocol developed by Affymetrix (GeneChip® Eukaryotic Small Sample Target Labeling Assay Version II; Affymetrix, Santa Clara, CA, USA).

growth_protocol: We analyzed the LCM motor neurons from the lumbar spinal tract of transplanted SMA mice (n=3), untransplanted SMA mice (n=3) and wt (n=3). The latter groups underwent surgical procedure with vehicle. The surgical procedure and cell transplantation was done at P1 and the animals were sacrificed at 13 days. Spinal cords (lumbar regions L1–L5) of perfused with PFA mice were rapidly removed, embedded in Tissue-Tek OCT Compound (Zoeterwoude, the Netherlands) and frozen in liquid Nitrogen and stored at -80°C. Tissues were sectioned at 16 μm and mounted on covered membrane slides (Leica). The sections were stored at –80°C until microdissection.

extract_protocol: Total RNA from the microdissected motoneurons was isolated using RNeasy® Micro Kit (Qiagen, Valencia, CA, USA) including Dnase treatment to remove potential genomic DNA contamination.

treatment_protocol: Motoneurons were microdissected using the Leica Laser Microdissection Microscope – ASLMD (Leica). Motoneurones were microdissected using the laser microdissector recovering device (ASLMD). Motoneurones were catapulted into a microfuge cap moistened with a drop of mineral oil (Sigma Chemical, Saint Louis, USA). Approximately 100 cells were collected per cap. Motoneurones were pooled from one animal per GeneChip.

tag: SMA mice, SMN2+/+;SmnΔ7+/+;mSmn -/- (line 4299; FVB.Cg-Tg(SMN2*delta7)4299Ahmb Tg(SMN2)89Ahmb Smn1tm1Msd


title: Motorneuron_TranslplantedSMA_sample1

description: NSC-transplanted SMA mouse motoneurons

source_name: NSC-transplanted SMA mouse motoneurons


title: Motorneuron_TranslplantedSMA_sample2

description: NSC-transplanted SMA mouse motoneurons


title: Motorneuron_TranslplantedSMA_sample3

description: NSC-transplanted SMA mouse motoneurons


title: Motorneuron_SMA_sample1

description: veichle-treated SMA mouse motoneurons


title: Suz12_PC3_2

city: Rehovot

first: Amos

last: Tanay

address: The Weizmann Insititute

department: Computer Science and Applied Math

country: Israel

institute: The Weizmann Institute

description: Nimblegen Inc.

hyb_protocol: Nimblegen Inc.

scan_protocol: Nimblegen Inc.

data_processing: ChIP: MeDIP data was normalized as described in Gal Yam et al. 2008. Briefly, channel intensities were quantile normalized to eliminate correlation a) between  raw input intensity and binding ratios and b) between probes' G and C contents and their binding ratios.

source_name: PC3 DNA

label_protocol: See Nimblegen Inc.

extract_protocol: Sonicated DNA

tag: PC3 sonicated chromatin

source_name: PC3 Suz12 ChIP

extract_protocol: Cells were cross linked with 1% formaldehyde for 15 min at room temperature followed by quenching with 0.125 M glycine. Cross linked cells were washed twice with ice-cold PBS, once with lysis buffer  1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% triton x-100, protease inhibitors(Complete, Roche)) and once with lysis buffer 2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA, 10 mM Tris pH 8, protease inhibitors) . Washings with buffers 1 and 2 consisted of a 10 min rotation and a 7 min spin at 500xg (1,200 rpm) at 40 C. The resulting nuclei were lysed with ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1) and sonicated. Sonicated chromatin (200µg for RNA PolII and SUZ12 ChIP and 25 µg for H3K27me3) was diluted 10 times with ChIP dilution buffer ( 0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.1, 167 mM NaCl) incubated overnight at 40C with 10 µg of antibody preincubated with 100µl of either sheep anti-mouse IgG or sheep anti-rabbit IgG coated Dynabeads (M-280, Invitrogen). ChIP antibodies used were: anti SUZ12 (07-379, Upstate biotechnologies), and anti H3K27me3 (Abcam). Following incubation the beads were washed 5-8 times with RIPA buffer and once with TE followed by elution, de-crosslinking, and proteinase K treatment. DNA was purified by phenol chloroform extraction and ethanol precipitation. For array experiments output and input DNA were incubated with RNase A (0.3 µg/µl) for 2h at 37°C and re-purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA). 40 l of output  DNA and 20 ng of input DNA were used for one round of linker mediated PCR amplification (LM-PCR) as previously described. The following conditions were used for the PCR amplification: 55°C for 2 min, 72°C for 5 min, 95°C for 2 min, 95°C for 1min, 60°C for 1min, 72°C for 2 min (repeat step 4-6 22 times), 72°C for 5 min. The amplified DNA was purified using the QIAquick PCR purification kit and labeled and hybridized to our custom array by Nimblegen. ChIP and array experiments were done in duplicates.

tag: PC3 Suz12 ChIP-enriched DNA


title: Suz12_PrEC_2

description: Nimblegen Inc.

source_name: PrEC DNA

tag: PrEC sonicated chromatin

source_name: PrEC Suz12 ChIP

tag: PrEC Suz12 ChIP-enriched DNA


title: Motorneuron_wildtype_sample3

description: veichle-treated wildtype mouse motoneurons

tag: SMA mice, SMN2+/+;SmnΔ7+/+;mSmn+/− (line 4299; FVB.Cg-Tg(SMN2*delta7)4299Ahmb Tg(SMN2)89Ahmb Smn1tm1Msd


title: ectopic p73 binding sites

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: ChIPSeq experiment was contracted to GenPathway, Inc, San Diego, CA. Raw data files are not available.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Genpathway FactorPath DiscoveryMode.
In this data, values are normalized to input (non-IP) DNA. p73 binding to proprietary control regions was used to confirm low background in the ChIP assay. Three regions to which p73 is bound were compared to a control region of the genome. Specificity was tested using the following genomic regions, and the following data normalized to input values.  Binding Events Detected Per 1000 Cells: Control Region = 0.01, MDM2 = 29.72, CDKN1A = 13.97, p53R2 = 9.37.  Standard Deviation:  Control = 0.01, MDM2 = 4.59, CDKN1A = 2.65, and p53R2 = 1.52.
Values are expressed as the number of alignments in any given cluster of tags.

label: not applicable

source_name: H1299 cells, p73 IP sample

label_protocol: not applicable

growth_protocol: cell culture H1299 cells

extract_protocol: formaldehyde crosslinking and crosslink reversal

treatment_protocol: transduced with TAp73beta expressing adenovirus for 5 h

tag: cancer cell line


title: Motorneuron_wildtype_sample1

source_name: veichle-treated wildtype mouse motoneurons


title: MM_0250_A

status: Public on Aug 05 2008

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Newly diagnosed patients

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: For each membrane, the data were normalized by the global intensity hybridization. A background value was calculated from negative controls median ± 6 SD and subtracted to each value. After expression data correction for the amount of PCR product spotted onto the membrane, only features detected in at least 5% of the patients were retained for subsequent analysis. Finally, values are log2-transformed. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).

source_name: MM_0250_A Bone marrow

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.

extract_protocol: Mononuclear bone marrow cells were separated using gradient density centrifugation (lymphocyte separation medium, Eurobio, Les Ulis, France), and plasmacytosis was evaluated by morphology in these mononuclear cell suspensions. Plasma cells (PCs) were then positively selected using anti-CD138–coated microbeads (Miltenyi, Paris, France), because CD138 is expressed only on PCs (normal and malignant) within the bone marrow. Purity and viability of the positively selected cell suspension was assessed by morphology and was above 96% in all the cases. One million PCs were used to prepare total RNA using the guanidinium thiocyanate–phenol method. The RNA integrity was randomly verified by using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: Tumor

value: multiple myeloma. Tissue:bone marrow. Cells:purified CD138+ plasma cells.


title: 5mC_SSSI_1

description: Nimblegen Inc.

data_processing: MeDIP: MeDIP data was normalized as described in Gal Yam et al. 2008. Briefly, raw channel intensities were quantile normalized and then combined into a detailed model that expresses the correlation between probe's CpG content, probe's G+C content and array binding ratio. binding ratios were corrected using data on MeDIP of DNA that was treated with M.SssI to full methylation.

tag: PC3, M.SssI treated Input DNA

source_name: PC3 M.SssI treated MeDIP

extract_protocol: 10 micro-g of sonicated genomic DNA (100-400 bp length) was denatured, incubated O/N at 4oC with 20 ug of anti-methyl cytosine  antibody (Diagenode, Belgium), and subsequently with 60 µl of Protein A/G beads (Upstate Biotechnologies, Charlottesville, VA) for 2h at 4oC. The beads were washed and incubated with digestion buffer and proteinase k for 3h and the DNA extracted by phenol-chloroform and EtOH precipitation. For array experiments the output from 3 MeDIP reactions was combined (total of 30 µg starting DNA) to constitute one replicate to eliminate the need for whole genome amplification.

treatment_protocol: For the M.SssI controls, human genomic DNA was treated with M.SssI (4 units per 1µg DNA, New England Biolabs) for 4h prior to sonication and immunoprecipitation as described above. The output of 2 MeDIP reactions performed on M.SssI treated DNA (total of 20 µg starting DNA) was combined to constitute one replicate. Sonicated M.SssI treated DNA served as the input.

tag: PC3, M.SssI treated and MeDIP enriched DNA


title: Motorneuron_SMA_sample2

description: veichle-treated SMA mouse motoneurons


title: MM_0249_A

description: Newly diagnosed patients

source_name: MM_0249_A Bone marrow


title: MM_0248_A

description: Newly diagnosed patients

source_name: MM_0248_A Bone marrow


title: Suz12_PrEC_1

description: Nimblegen Inc.


title: Motorneuron_wildtype_sample2


title: Suz12_PC3_1

description: Nimblegen Inc.


title: H3K27me3_PrEC_1

description: Nimblegen Inc.

tag: PrEC sonicated DNA

source_name: PrEC K27me3 ChIP

tag: PrEC H3K27me3 ChIP-enriched DNA


title: 5mC_PC3_3

description: Nimblegen Inc.

tag: PC3 input DNA

source_name: PC3 MeDIP

tag: PC3 MedIP enriched DNA


title: 5mC_PrEC_2

description: Nimblegen Inc.

tag: PrEC input DNA

source_name: PrEC MeDIP

tag: PrEC MedIP enriched DNA


title: MM_0247_A

description: Newly diagnosed patients

source_name: MM_0247_A Bone marrow


title: MM_0245_A

description: Newly diagnosed patients

source_name: MM_0245_A Bone marrow


title: H3K27me3_PC3_2

description: Nimblegen Inc.

tag: PC3 sonicated DNA

source_name: PC3 K27me3 ChIP

tag: PC3 K27me3 ChIP-enriched chromatin


title: H3K27me3_PrEC_2

description: Nimblegen Inc.

tag: PrEC H3K27me3 ChIP-enriched chromatin


title: 5mC_PrEC_1

description: Nimblegen Inc.

tag: PrEC Medip enriched DNA


title: MM_0244_A

description: Newly diagnosed patients

source_name: MM_0244_A Bone marrow


title: MM_0240_A

description: Newly diagnosed patients

source_name: MM_0240_A Bone marrow


title: 5mC_PrEC_3

description: Nimblegen Inc.


title: 5mC_SSSI_3

description: Nimblegen Inc.

source_name: PC3 DNA

tag: PC3 M.SssI treated input DNA

tag: PC3 M.SssI treated and MeDIP enriched DNA


title: MM_0239_A

description: Newly diagnosed patients

source_name: MM_0239_A Bone marrow


title: 5mC_PC3_2

description: Nimblegen Inc.

tag: PC3 MeDIP enriched DNA


title: MM_0242_A

description: Newly diagnosed patients

source_name: MM_0242_A Bone marrow


title: H3K27me3_PC3_1

description: Nimblegen Inc.

tag: PC3 Sonicated DNA

tag: PC3 K27me3 ChIP-enriched chromaitin


title: MM_0238_A

description: Newly diagnosed patients

source_name: MM_0238_A Bone marrow

tag: Tumor


title: MM_0243_A

description: Newly diagnosed patients

source_name: MM_0243_A Bone marrow


title: MM_0237_A

description: Newly diagnosed patients

source_name: MM_0237_A Bone marrow


title: MM_0235_A

description: Newly diagnosed patients

source_name: MM_0235_A Bone marrow


title: MM_0241_A

description: Newly diagnosed patients

source_name: MM_0241_A Bone marrow


title: MM_0236_A

description: Newly diagnosed patients

source_name: MM_0236_A Bone marrow


title: 5mC_PC3_1

description: Nimblegen Inc.

tag: PC3 extracted DNA


title: MM_0234_A

description: Newly diagnosed patients

source_name: MM_0234_A Bone marrow


title: MM_0232_A

description: Newly diagnosed patients

source_name: MM_0232_A Bone marrow


title: MM_0233_A

description: Newly diagnosed patients

source_name: MM_0233_A Bone marrow


title: MM_0230_A

description: Newly diagnosed patients

source_name: MM_0230_A Bone marrow


title: MM_0231_A

description: Newly diagnosed patients

source_name: MM_0231_A Bone marrow


title: MM_0229_A

description: Newly diagnosed patients

source_name: MM_0229_A Bone marrow


title: MM_0228_A

description: Newly diagnosed patients

source_name: MM_0228_A Bone marrow


title: MM_0226_A

description: Newly diagnosed patients

source_name: MM_0226_A Bone marrow


title: MM_0227_A

description: Newly diagnosed patients

source_name: MM_0227_A Bone marrow


title: 5mC_SSSI_2

description: Nimblegen Inc.

source_name: PC3 DNA

source_name: PC3 M.SssI treated MeDIP


title: MM_0225_A

description: Newly diagnosed patients

source_name: MM_0225_A Bone marrow


title: MM_0224_A

description: Newly diagnosed patients

source_name: MM_0224_A Bone marrow


title: MM_0223_A

description: Newly diagnosed patients

source_name: MM_0223_A Bone marrow


title: MM_0222_A

description: Newly diagnosed patients

source_name: MM_0222_A Bone marrow


title: MM_0219_A

description: Newly diagnosed patients

source_name: MM_0219_A Bone marrow


title: MM_0220_A

description: Newly diagnosed patients

source_name: MM_0220_A Bone marrow


title: MM_0221_A

description: Newly diagnosed patients

source_name: MM_0221_A Bone marrow


title: MM_0218_A

description: Newly diagnosed patients

source_name: MM_0218_A Bone marrow


title: MM_0212_A

description: Newly diagnosed patients

source_name: MM_0212_A Bone marrow


title: MM_0214_A

description: Newly diagnosed patients

source_name: MM_0214_A Bone marrow


title: MM_0215_A

description: Newly diagnosed patients

source_name: MM_0215_A Bone marrow


title: MM_0213_A

description: Newly diagnosed patients

source_name: MM_0213_A Bone marrow


title: MM_0216_A

description: Newly diagnosed patients

source_name: MM_0216_A Bone marrow


title: MM_0217_A

description: Newly diagnosed patients

source_name: MM_0217_A Bone marrow


title: MM_0211_A

description: Newly diagnosed patients

source_name: MM_0211_A Bone marrow


title: MM_0210_A

description: Newly diagnosed patients

source_name: MM_0210_A Bone marrow


title: MM_0209_A

description: Newly diagnosed patients

source_name: MM_0209_A Bone marrow


title: MM_0207_A

description: Newly diagnosed patients

source_name: MM_0207_A Bone marrow


title: MM_0206_A

description: Newly diagnosed patients

source_name: MM_0206_A Bone marrow


title: MM_0208_A

description: Newly diagnosed patients

source_name: MM_0208_A Bone marrow


title: MM_0205_A

description: Newly diagnosed patients

source_name: MM_0205_A Bone marrow


title: MM_0202_A

description: Newly diagnosed patients

source_name: MM_0202_A Bone marrow


title: MM_0203_A

description: Newly diagnosed patients

source_name: MM_0203_A Bone marrow


title: MM_0204_A

description: Newly diagnosed patients

source_name: MM_0204_A Bone marrow


title: MM_0200_A

description: Newly diagnosed patients

source_name: MM_0200_A Bone marrow


title: MM_0199_A

description: Newly diagnosed patients

source_name: MM_0199_A Bone marrow


title: MM_0196_A

description: Newly diagnosed patients

source_name: MM_0196_A Bone marrow


title: MM_0201_A

description: Newly diagnosed patients

source_name: MM_0201_A Bone marrow


title: MM_0197_A

description: Newly diagnosed patients

source_name: MM_0197_A Bone marrow


title: MM_0198_A

description: Newly diagnosed patients

source_name: MM_0198_A Bone marrow


title: MM_0194_A

description: Newly diagnosed patients

source_name: MM_0194_A Bone marrow


title: MM_0195_A

description: Newly diagnosed patients

source_name: MM_0195_A Bone marrow


title: MM_0191_A

description: Newly diagnosed patients

source_name: MM_0191_A Bone marrow


title: MM_0193_A

description: Newly diagnosed patients

source_name: MM_0193_A Bone marrow


title: MM_0192_A

description: Newly diagnosed patients

source_name: MM_0192_A Bone marrow


title: MM_0184_A

description: Newly diagnosed patients

source_name: MM_0184_A Bone marrow


title: MM_0183_A

description: Newly diagnosed patients

source_name: MM_0183_A Bone marrow


title: MM_0185_A

description: Newly diagnosed patients

source_name: MM_0185_A Bone marrow


title: MM_0186_A

description: Newly diagnosed patients

source_name: MM_0186_A Bone marrow


title: MM_0180_A

description: Newly diagnosed patients

source_name: MM_0180_A Bone marrow


title: MM_0189_A

description: Newly diagnosed patients

source_name: MM_0189_A Bone marrow


title: MM_0190_A

description: Newly diagnosed patients

source_name: MM_0190_A Bone marrow


title: MM_0179_A

description: Newly diagnosed patients

source_name: MM_0179_A Bone marrow


title: MM_0178_A

description: Newly diagnosed patients

source_name: MM_0178_A Bone marrow


title: MM_0187_A

description: Newly diagnosed patients

source_name: MM_0187_A Bone marrow


title: MM_0177_A

description: Newly diagnosed patients

source_name: MM_0177_A Bone marrow


title: MM_0188_A

description: Newly diagnosed patients

source_name: MM_0188_A Bone marrow


title: MM_0181_A

description: Newly diagnosed patients

source_name: MM_0181_A Bone marrow


title: MM_0175_A

description: Newly diagnosed patients

source_name: MM_0175_A Bone marrow


title: MM_0171_A

description: Newly diagnosed patients

source_name: MM_0171_A Bone marrow


title: MM_0182_A

description: Newly diagnosed patients

source_name: MM_0182_A Bone marrow


title: MM_0176_A

description: Newly diagnosed patients

source_name: MM_0176_A Bone marrow


title: MM_0173_A

description: Newly diagnosed patients

source_name: MM_0173_A Bone marrow


title: MM_0174_A

description: Newly diagnosed patients

source_name: MM_0174_A Bone marrow


title: MM_0168_A

description: Newly diagnosed patients

source_name: MM_0168_A Bone marrow


title: MM_0169_A

description: Newly diagnosed patients

source_name: MM_0169_A Bone marrow


title: MM_0170_A

description: Newly diagnosed patients

source_name: MM_0170_A Bone marrow


title: MM_0167_A

description: Newly diagnosed patients

source_name: MM_0167_A Bone marrow


title: MM_0166_A

description: Newly diagnosed patients

source_name: MM_0166_A Bone marrow


title: MM_0246_A

description: Newly diagnosed patients

source_name: MM_0246_A Bone marrow


title: MM_0159_A

description: Newly diagnosed patients

source_name: MM_0159_A Bone marrow


title: MM_0163_A

description: Newly diagnosed patients

source_name: MM_0163_A Bone marrow


title: MM_0160_A

description: Newly diagnosed patients

source_name: MM_0160_A Bone marrow


title: MM_0165_A

description: Newly diagnosed patients

source_name: MM_0165_A Bone marrow


title: MM_0161_A

description: Newly diagnosed patients

source_name: MM_0161_A Bone marrow


title: MM_0162_A

description: Newly diagnosed patients

source_name: MM_0162_A Bone marrow


title: MM_0158_A

description: Newly diagnosed patients

source_name: MM_0158_A Bone marrow


title: MM_0164_A

description: Newly diagnosed patients

source_name: MM_0164_A Bone marrow


title: MM_0172_A

description: Newly diagnosed patients

source_name: MM_0172_A Bone marrow


title: MM_0156_A

description: Newly diagnosed patients

source_name: MM_0156_A Bone marrow


title: MM_0153_A

description: Newly diagnosed patients

source_name: MM_0153_A Bone marrow


title: MM_0154_A

description: Newly diagnosed patients

source_name: MM_0154_A Bone marrow


title: MM_0148_A

description: Newly diagnosed patients

source_name: MM_0148_A Bone marrow


title: MM_0152_A

description: Newly diagnosed patients

source_name: MM_0152_A Bone marrow


title: MM_0149_A

description: Newly diagnosed patients

source_name: MM_0149_A Bone marrow


title: MM_0151_A

description: Newly diagnosed patients

source_name: MM_0151_A Bone marrow


title: MM_0147_A

description: Newly diagnosed patients

source_name: MM_0147_A Bone marrow


title: MM_0157_A

description: Newly diagnosed patients

source_name: MM_0157_A Bone marrow


title: MM_0145_A

description: Newly diagnosed patients

source_name: MM_0145_A Bone marrow


title: MM_0144_A

description: Newly diagnosed patients

source_name: MM_0144_A Bone marrow


title: MM_0142_A

description: Newly diagnosed patients

source_name: MM_0142_A Bone marrow


title: MM_0141_A

description: Newly diagnosed patients

source_name: MM_0141_A Bone marrow


title: MM_0140_A

description: Newly diagnosed patients

source_name: MM_0140_A Bone marrow


title: MM_0139_A

description: Newly diagnosed patients

source_name: MM_0139_A Bone marrow


title: MM_0143_A

description: Newly diagnosed patients

source_name: MM_0143_A Bone marrow


title: MM_0146_A

description: Newly diagnosed patients

source_name: MM_0146_A Bone marrow


title: MM_0138_A

description: Newly diagnosed patients

source_name: MM_0138_A Bone marrow


title: MM_0137_A

description: Newly diagnosed patients

source_name: MM_0137_A Bone marrow


title: MM_0136_A

description: Newly diagnosed patients

source_name: MM_0136_A Bone marrow


title: MM_0150_A

description: Newly diagnosed patients

source_name: MM_0150_A Bone marrow


title: MM_0155_A

description: Newly diagnosed patients

source_name: MM_0155_A Bone marrow


title: MM_0132_A

description: Newly diagnosed patients

source_name: MM_0132_A Bone marrow


title: MM_0133_A

description: Newly diagnosed patients

source_name: MM_0133_A Bone marrow


title: MM_0130_A

description: Newly diagnosed patients

source_name: MM_0130_A Bone marrow


title: MM_0135_A

description: Newly diagnosed patients

source_name: MM_0135_A Bone marrow


title: MM_0131_A

description: Newly diagnosed patients

source_name: MM_0131_A Bone marrow


title: MM_0129_A

description: Newly diagnosed patients

source_name: MM_0129_A Bone marrow


title: MM_0127_A

description: Newly diagnosed patients

source_name: MM_0127_A Bone marrow


title: MM_0128_A

description: Newly diagnosed patients

source_name: MM_0128_A Bone marrow


title: MM_0126_A

description: Newly diagnosed patients

source_name: MM_0126_A Bone marrow


title: MM_0125_A

description: Newly diagnosed patients

source_name: MM_0125_A Bone marrow


title: MM_0124_A

description: Newly diagnosed patients

source_name: MM_0124_A Bone marrow


title: MM_0134_A

description: Newly diagnosed patients

source_name: MM_0134_A Bone marrow


title: MM_0120_A

description: Newly diagnosed patients

source_name: MM_0120_A Bone marrow


title: MM_0118_A

description: Newly diagnosed patients

source_name: MM_0118_A Bone marrow


title: MM_0122_A

description: Newly diagnosed patients

source_name: MM_0122_A Bone marrow


title: MM_0119_A

description: Newly diagnosed patients

source_name: MM_0119_A Bone marrow


title: MM_0121_A

description: Newly diagnosed patients

source_name: MM_0121_A Bone marrow


title: MM_0123_A

description: Newly diagnosed patients

source_name: MM_0123_A Bone marrow


title: MM_0116_A

description: Newly diagnosed patients

source_name: MM_0116_A Bone marrow


title: MM_0115_A

description: Newly diagnosed patients

source_name: MM_0115_A Bone marrow


title: MM_0114_A

description: Newly diagnosed patients

source_name: MM_0114_A Bone marrow


title: MM_0106_A

description: Newly diagnosed patients

source_name: MM_0106_A Bone marrow


title: MM_0112_A

description: Newly diagnosed patients

source_name: MM_0112_A Bone marrow


title: MM_0110_A

description: Newly diagnosed patients

source_name: MM_0110_A Bone marrow


title: MM_0107_A

description: Newly diagnosed patients

source_name: MM_0107_A Bone marrow


title: MM_0109_A

description: Newly diagnosed patients

source_name: MM_0109_A Bone marrow


title: MM_0108_A

description: Newly diagnosed patients

source_name: MM_0108_A Bone marrow


title: MM_0105_A

description: Newly diagnosed patients

source_name: MM_0105_A Bone marrow


title: MM_0111_A

description: Newly diagnosed patients

source_name: MM_0111_A Bone marrow


title: MM_0117_A

description: Newly diagnosed patients

source_name: MM_0117_A Bone marrow


title: MM_0102_A

description: Newly diagnosed patients

source_name: MM_0102_A Bone marrow


title: MM_0104_A

description: Newly diagnosed patients

source_name: MM_0104_A Bone marrow


title: MM_0113_A

description: Newly diagnosed patients

source_name: MM_0113_A Bone marrow


title: MM_0101_A

description: Newly diagnosed patients

source_name: MM_0101_A Bone marrow


title: MM_0097_A

description: Newly diagnosed patients

source_name: MM_0097_A Bone marrow


title: MM_0100_A

description: Newly diagnosed patients

source_name: MM_0100_A Bone marrow


title: MM_0099_A

description: Newly diagnosed patients

source_name: MM_0099_A Bone marrow


title: MM_0096_A

description: Newly diagnosed patients

source_name: MM_0096_A Bone marrow


title: MM_0103_A

description: Newly diagnosed patients

source_name: MM_0103_A Bone marrow


title: MM_0092_A

description: Newly diagnosed patients

source_name: MM_0092_A Bone marrow


title: MM_0095_A

description: Newly diagnosed patients

source_name: MM_0095_A Bone marrow


title: MM_0098_A

description: Newly diagnosed patients

source_name: MM_0098_A Bone marrow


title: MM_0093_A

description: Newly diagnosed patients

source_name: MM_0093_A Bone marrow


title: MM_0091_A

description: Newly diagnosed patients

source_name: MM_0091_A Bone marrow


title: MM_0090_A

description: Newly diagnosed patients

source_name: MM_0090_A Bone marrow


title: MM_0094_A

description: Newly diagnosed patients

source_name: MM_0094_A Bone marrow


title: MM_0089_A

description: Newly diagnosed patients

source_name: MM_0089_A Bone marrow


title: MM_0085_A

description: Newly diagnosed patients

source_name: MM_0085_A Bone marrow


title: MM_0084_A

description: Newly diagnosed patients

source_name: MM_0084_A Bone marrow


title: MM_0086_A

description: Newly diagnosed patients

source_name: MM_0086_A Bone marrow


title: MM_0082_A

description: Newly diagnosed patients

source_name: MM_0082_A Bone marrow


title: MM_0079_A

description: Newly diagnosed patients

source_name: MM_0079_A Bone marrow


title: MM_0080_A

description: Newly diagnosed patients

source_name: MM_0080_A Bone marrow


title: MM_0083_A

description: Newly diagnosed patients

source_name: MM_0083_A Bone marrow


title: MM_0081_A

description: Newly diagnosed patients

source_name: MM_0081_A Bone marrow


title: MM_0087_A

description: Newly diagnosed patients

source_name: MM_0087_A Bone marrow


title: MM_0088_A

description: Newly diagnosed patients

source_name: MM_0088_A Bone marrow


title: MM_0076_A

description: Newly diagnosed patients

source_name: MM_0076_A Bone marrow


title: MM_0072_A

description: Newly diagnosed patients

source_name: MM_0072_A Bone marrow


title: MM_0078_A

description: Newly diagnosed patients

source_name: MM_0078_A Bone marrow


title: MM_0077_A

description: Newly diagnosed patients

source_name: MM_0077_A Bone marrow


title: MM_0074_A

description: Newly diagnosed patients

source_name: MM_0074_A Bone marrow


title: MM_0075_A

description: Newly diagnosed patients

source_name: MM_0075_A Bone marrow


title: MM_0073_A

description: Newly diagnosed patients

source_name: MM_0073_A Bone marrow


title: MM_0071_A

description: Newly diagnosed patients

source_name: MM_0071_A Bone marrow


title: MM_0068_A

description: Newly diagnosed patients

source_name: MM_0068_A Bone marrow


title: MM_0069_A

description: Newly diagnosed patients

source_name: MM_0069_A Bone marrow


title: MM_0067_A

description: Newly diagnosed patients

source_name: MM_0067_A Bone marrow


title: MM_0065_A

description: Newly diagnosed patients

source_name: MM_0065_A Bone marrow


title: MM_0070_A

description: Newly diagnosed patients

source_name: MM_0070_A Bone marrow


title: MM_0064_A

description: Newly diagnosed patients

source_name: MM_0064_A Bone marrow


title: MM_0063_A

description: Newly diagnosed patients

source_name: MM_0063_A Bone marrow


title: MM_0061_A

description: Newly diagnosed patients

source_name: MM_0061_A Bone marrow


title: MM_0066_A

description: Newly diagnosed patients

source_name: MM_0066_A Bone marrow


title: MM_0056_A

description: Newly diagnosed patients

source_name: MM_0056_A Bone marrow


title: MM_0062_A

description: Newly diagnosed patients

source_name: MM_0062_A Bone marrow


title: MM_0058_A

description: Newly diagnosed patients

source_name: MM_0058_A Bone marrow


title: MM_0057_A

description: Newly diagnosed patients

source_name: MM_0057_A Bone marrow


title: MM_0055_A

description: Newly diagnosed patients

source_name: MM_0055_A Bone marrow


title: MM_0054_A

description: Newly diagnosed patients

source_name: MM_0054_A Bone marrow


title: MM_0060_A

description: Newly diagnosed patients

source_name: MM_0060_A Bone marrow


title: MM_0053_A

description: Newly diagnosed patients

source_name: MM_0053_A Bone marrow


title: MM_0050_A

description: Newly diagnosed patients

source_name: MM_0050_A Bone marrow


title: MM_0059_A

description: Newly diagnosed patients

source_name: MM_0059_A Bone marrow


title: MM_0051_A

description: Newly diagnosed patients

source_name: MM_0051_A Bone marrow


title: MM_0052_A

description: Newly diagnosed patients

source_name: MM_0052_A Bone marrow


title: MM_0045_A

description: Newly diagnosed patients

source_name: MM_0045_A Bone marrow


title: MM_0048_A

description: Newly diagnosed patients

source_name: MM_0048_A Bone marrow


title: MM_0049_A

description: Newly diagnosed patients

source_name: MM_0049_A Bone marrow


title: MM_0047_A

description: Newly diagnosed patients

source_name: MM_0047_A Bone marrow


title: MM_0044_A

description: Newly diagnosed patients

source_name: MM_0044_A Bone marrow


title: MM_0043_A

description: Newly diagnosed patients

source_name: MM_0043_A Bone marrow


title: MM_0041_A

description: Newly diagnosed patients

source_name: MM_0041_A Bone marrow


title: MM_0040_A

description: Newly diagnosed patients

source_name: MM_0040_A Bone marrow


title: MM_0039_A

description: Newly diagnosed patients

source_name: MM_0039_A Bone marrow


title: MM_0046_A

description: Newly diagnosed patients

source_name: MM_0046_A Bone marrow


title: MM_0042_A

description: Newly diagnosed patients

source_name: MM_0042_A Bone marrow


title: MM_0038_A

description: Newly diagnosed patients

source_name: MM_0038_A Bone marrow


title: MM_0035_A

description: Newly diagnosed patients

source_name: MM_0035_A Bone marrow


title: MM_0036_A

description: Newly diagnosed patients

source_name: MM_0036_A Bone marrow


title: MM_0037_A

description: Newly diagnosed patients

source_name: MM_0037_A Bone marrow


title: MM_0034_A

description: Newly diagnosed patients

source_name: MM_0034_A Bone marrow


title: MM_0033_A

description: Newly diagnosed patients

source_name: MM_0033_A Bone marrow


title: MM_0020_A

description: Newly diagnosed patients

source_name: MM_0020_A Bone marrow


title: MM_0024_A

description: Newly diagnosed patients

source_name: MM_0024_A Bone marrow


title: MM_0023_A

description: Newly diagnosed patients

source_name: MM_0023_A Bone marrow


title: MM_0030_A

description: Newly diagnosed patients

source_name: MM_0030_A Bone marrow


title: MM_0031_A

description: Newly diagnosed patients

source_name: MM_0031_A Bone marrow


title: MM_0022_A

description: Newly diagnosed patients

source_name: MM_0022_A Bone marrow


title: MM_0021_A

description: Newly diagnosed patients

source_name: MM_0021_A Bone marrow


title: MM_0028_A

description: Newly diagnosed patients

source_name: MM_0028_A Bone marrow


title: MM_0029_A

description: Newly diagnosed patients

source_name: MM_0029_A Bone marrow


title: MM_0026_A

description: Newly diagnosed patients

source_name: MM_0026_A Bone marrow


title: MM_0032_A

description: Newly diagnosed patients

source_name: MM_0032_A Bone marrow


title: MM_0019_A

description: Newly diagnosed patients

source_name: MM_0019_A Bone marrow


title: MM_0027_A

description: Newly diagnosed patients

source_name: MM_0027_A Bone marrow


title: MM_0015_A

description: Newly diagnosed patients

source_name: MM_0015_A Bone marrow


title: MM_0016_A

description: Newly diagnosed patients

source_name: MM_0016_A Bone marrow


title: MM_0017_A

description: Newly diagnosed patients

source_name: MM_0017_A Bone marrow


title: MM_0014_A

description: Newly diagnosed patients

source_name: MM_0014_A Bone marrow


title: MM_0013_A

description: Newly diagnosed patients

source_name: MM_0013_A Bone marrow


title: MM_0025_A

description: Newly diagnosed patients

source_name: MM_0025_A Bone marrow


title: MM_0008_A

description: Newly diagnosed patients

source_name: MM_0008_A Bone marrow


title: MM_0018_A

description: Newly diagnosed patients

source_name: MM_0018_A Bone marrow


title: MM_0011_A

description: Newly diagnosed patients

source_name: MM_0011_A Bone marrow


title: MM_0012_A

description: Newly diagnosed patients

source_name: MM_0012_A Bone marrow


title: MM_0010_A

description: Newly diagnosed patients

source_name: MM_0010_A Bone marrow


title: MM_0009_A

description: Newly diagnosed patients

source_name: MM_0009_A Bone marrow


title: MM_0005_A

description: Newly diagnosed patients

source_name: MM_0005_A Bone marrow


title: MM_0006_A

description: Newly diagnosed patients

source_name: MM_0006_A Bone marrow


title: MM_0003_A

description: Newly diagnosed patients

source_name: MM_0003_A Bone marrow


title: MM_0007_A

description: Newly diagnosed patients

source_name: MM_0007_A Bone marrow


title: MM_0004_A

description: Newly diagnosed patients

source_name: MM_0004_A Bone marrow


title: MM_0248_B

description: Newly diagnosed patients

data_processing: For each membrane, the data were normalized by the global intensity hybridization. A background value was calculated from negative controls median ± 6 SD and subtracted to each value. After expression data correction for the amount of PCR product spotted onto the membrane, only features detected in at least 5% of the patients were retained for subsequent analysis. Finally, values are log2-transformed.

source_name: MM_0248_B Bone marrow


title: MM_0246_B

description: Newly diagnosed patients

source_name: MM_0246_B Bone marrow


title: MM_0241_B

description: Newly diagnosed patients

source_name: MM_0241_B Bone marrow


title: MM_0002_A

description: Newly diagnosed patients

source_name: MM_0002_A Bone marrow


title: MM_0247_B

description: Newly diagnosed patients

source_name: MM_0247_B Bone marrow


title: MM_0243_B

description: Newly diagnosed patients

source_name: MM_0243_B Bone marrow


title: MM_0242_B

description: Newly diagnosed patients

source_name: MM_0242_B Bone marrow


title: MM_0239_B

description: Newly diagnosed patients

source_name: MM_0239_B Bone marrow


title: MM_0244_B

description: Newly diagnosed patients

source_name: MM_0244_B Bone marrow


title: MM_0240_B

description: Newly diagnosed patients

source_name: MM_0240_B Bone marrow


title: MM_0245_B

description: Newly diagnosed patients

source_name: MM_0245_B Bone marrow


title: MM_0250_B

description: Newly diagnosed patients

source_name: MM_0250_B Bone marrow


title: MM_0001_A

description: Newly diagnosed patients

data_processing:
For each membrane, the data were normalized by the global intensity hybridization.
A background value was calculated from negative controls median ± 6 SD and subtracted to each value.
After expression data correction for the amount of PCR product spotted onto the membrane, only features detected in at least 5% of the patients were retained for subsequent analysis. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).

source_name: MM_0001_A Bone marrow

extract_protocol:
Mononuclear bone marrow cells were separated using gradient density centrifugation (lymphocyte separation medium, Eurobio, Les Ulis, France), and plasmacytosis was evaluated by morphology in these mononuclear cell suspensions.
Plasma cells (PCs) were then positively selected using anti-CD138–coated microbeads (Miltenyi, Paris, France), because CD138 is expressed only on PCs (normal and malignant) within the bone marrow.
Purity and viability of the positively selected cell suspension was assessed by morphology and was above 96% in all the cases. One million PCs were used to prepare total RNA using the guanidinium thiocyanate–phenol method.
The RNA integrity was randomly verified by using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: multiple myeloma.

tag: Tissue

value: bone marrow.

tag: Cells

value: purified CD138+ plasma cells.


title: MM_0236_B

description: Newly diagnosed patients

source_name: MM_0236_B Bone marrow


title: MM_0238_B

description: Newly diagnosed patients

source_name: MM_0238_B Bone marrow


title: MM_0235_B

description: Newly diagnosed patients

source_name: MM_0235_B Bone marrow


title: MM_0233_B

description: Newly diagnosed patients

source_name: MM_0233_B Bone marrow


title: MM_0234_B

description: Newly diagnosed patients

source_name: MM_0234_B Bone marrow


title: MM_0232_B

description: Newly diagnosed patients

source_name: MM_0232_B Bone marrow


title: MM_0231_B

description: Newly diagnosed patients

source_name: MM_0231_B Bone marrow


title: MM_0229_B

description: Newly diagnosed patients

source_name: MM_0229_B Bone marrow


title: MM_0227_B

description: Newly diagnosed patients

source_name: MM_0227_B Bone marrow


title: MM_0228_B

description: Newly diagnosed patients

source_name: MM_0228_B Bone marrow


title: MM_0237_B

description: Newly diagnosed patients

source_name: MM_0237_B Bone marrow


title: MM_0223_B

description: Newly diagnosed patients

source_name: MM_0223_B Bone marrow


title: MM_0226_B

description: Newly diagnosed patients

source_name: MM_0226_B Bone marrow


title: MM_0220_B

description: Newly diagnosed patients

source_name: MM_0220_B Bone marrow


title: MM_0221_B

description: Newly diagnosed patients

source_name: MM_0221_B Bone marrow


title: MM_0217_B

description: Newly diagnosed patients

source_name: MM_0217_B Bone marrow


title: MM_0222_B

description: Newly diagnosed patients

source_name: MM_0222_B Bone marrow


title: MM_0216_B

description: Newly diagnosed patients

source_name: MM_0216_B Bone marrow


title: MM_0219_B

description: Newly diagnosed patients

source_name: MM_0219_B Bone marrow


title: MM_0225_B

description: Newly diagnosed patients

source_name: MM_0225_B Bone marrow


title: MM_0230_B

description: Newly diagnosed patients

source_name: MM_0230_B Bone marrow


title: MM_0215_B

description: Newly diagnosed patients

source_name: MM_0215_B Bone marrow


title: MM_0249_B

description: Newly diagnosed patients

source_name: MM_0249_B Bone marrow


title: MM_0218_B

description: Newly diagnosed patients

source_name: MM_0218_B Bone marrow


title: MM_0213_B

description: Newly diagnosed patients

source_name: MM_0213_B Bone marrow


title: MM_0212_B

description: Newly diagnosed patients

source_name: MM_0212_B Bone marrow


title: MM_0211_B

description: Newly diagnosed patients

source_name: MM_0211_B Bone marrow


title: MM_0224_B

description: Newly diagnosed patients

source_name: MM_0224_B Bone marrow


title: MM_0210_B

description: Newly diagnosed patients

source_name: MM_0210_B Bone marrow


title: MM_0214_B

description: Newly diagnosed patients

source_name: MM_0214_B Bone marrow


title: MM_0206_B

description: Newly diagnosed patients

source_name: MM_0206_B Bone marrow


title: MM_0207_B

description: Newly diagnosed patients

source_name: MM_0207_B Bone marrow


title: MM_0204_B

description: Newly diagnosed patients

source_name: MM_0204_B Bone marrow


title: MM_0205_B

description: Newly diagnosed patients

source_name: MM_0205_B Bone marrow


title: MM_0208_B

description: Newly diagnosed patients

source_name: MM_0208_B Bone marrow


title: MM_0209_B

description: Newly diagnosed patients

source_name: MM_0209_B Bone marrow


title: MM_0203_B

description: Newly diagnosed patients

source_name: MM_0203_B Bone marrow


title: MM_0201_B

description: Newly diagnosed patients

source_name: MM_0201_B Bone marrow


title: MM_0202_B

description: Newly diagnosed patients

source_name: MM_0202_B Bone marrow


title: MM_0196_B

description: Newly diagnosed patients

source_name: MM_0196_B Bone marrow


title: MM_0200_B

description: Newly diagnosed patients

source_name: MM_0200_B Bone marrow


title: MM_0198_B

description: Newly diagnosed patients

source_name: MM_0198_B Bone marrow


title: MM_0189_B

description: Newly diagnosed patients

source_name: MM_0189_B Bone marrow


title: MM_0192_B

description: Newly diagnosed patients

source_name: MM_0192_B Bone marrow


title: MM_0191_B

description: Newly diagnosed patients

source_name: MM_0191_B Bone marrow


title: MM_0193_B

description: Newly diagnosed patients

source_name: MM_0193_B Bone marrow


title: MM_0187_B

description: Newly diagnosed patients

source_name: MM_0187_B Bone marrow


title: MM_0188_B

description: Newly diagnosed patients

source_name: MM_0188_B Bone marrow


title: MM_0195_B

description: Newly diagnosed patients

source_name: MM_0195_B Bone marrow


title: MM_0186_B

description: Newly diagnosed patients

source_name: MM_0186_B Bone marrow


title: MM_0199_B

description: Newly diagnosed patients

source_name: MM_0199_B Bone marrow


title: MM_0197_B

description: Newly diagnosed patients

source_name: MM_0197_B Bone marrow


title: MM_0185_B

description: Newly diagnosed patients

source_name: MM_0185_B Bone marrow


title: MM_0190_B

description: Newly diagnosed patients

source_name: MM_0190_B Bone marrow


title: MM_0183_B

description: Newly diagnosed patients

source_name: MM_0183_B Bone marrow


title: MM_0194_B

description: Newly diagnosed patients

source_name: MM_0194_B Bone marrow


title: MM_0182_B

description: Newly diagnosed patients

source_name: MM_0182_B Bone marrow


title: Thymol treated 2

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.Hybridization solution was denatured at 95 for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42 overnight and washed with two consecutive solutions.

scan_protocol: LuxScanTM 3.0 software

data_processing: A space- and intensity-dependent normalization based on a LOWESS program,For further statistical analyses, The Significance Analysis of Microarrays (SAM ) add-in to Microsoft Excel was used to compare the replicate arrays experiments.

organism: Saccharomyces cerevisiae

source_name: Thymol treated 2

label_protocol: cDNA products subjected to transcription reactions .Klenow enzyme labeling strategy was adopted after reverse transcription.

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently, thymol stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the culture. Then, the yeast cells were further incubated for a certain time.

extract_protocol: Totole RNA was extracted by a hot acidic phenol method. Collart,M.A. & Oliviero, S. (1995). Preparation of yeast RNA.In Short Protocols in Molecular Biology, 3rd edn, (Ausubel F., Brent R., Kingston, R. T., Moode, D. D, Seidman, J. G., Smith, J. A. et al., Eds), pp. 13-46-13-47. John Wiley and Sons, Inc., New York, NY.

treatment_protocol: plant medcine thymol

tag: strain L1190 refer to the previous study done by liang zhang et al 2002 JAC

source_name: Saccharomyces cerevisiae_DMSO

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently,DMSO was added to the culture. Then, the yeast cells were further incubated for a certain time.

treatment_protocol: DMSO


title: MM_0180_B

description: Newly diagnosed patients

source_name: MM_0180_B Bone marrow


title: MM_0179_B

description: Newly diagnosed patients

source_name: MM_0179_B Bone marrow


title: Thymol treated 3

source_name: Thymol treated 3


title: MM_0181_B

description: Newly diagnosed patients

source_name: MM_0181_B Bone marrow


title: MM_0184_B

description: Newly diagnosed patients

source_name: MM_0184_B Bone marrow


title: MM_0171_B

description: Newly diagnosed patients

source_name: MM_0171_B Bone marrow


title: MM_0173_B

description: Newly diagnosed patients

source_name: MM_0173_B Bone marrow


title: MM_0169_B

description: Newly diagnosed patients

source_name: MM_0169_B Bone marrow


title: MM_0178_B

description: Newly diagnosed patients

source_name: MM_0178_B Bone marrow


title: MM_0168_B

description: Newly diagnosed patients

source_name: MM_0168_B Bone marrow


title: MM_0174_B

description: Newly diagnosed patients

source_name: MM_0174_B Bone marrow


title: MM_0177_B

description: Newly diagnosed patients

source_name: MM_0177_B Bone marrow


title: MM_0175_B

description: Newly diagnosed patients

source_name: MM_0175_B Bone marrow


title: MM_0176_B

description: Newly diagnosed patients

source_name: MM_0176_B Bone marrow


title: MM_0170_B

description: Newly diagnosed patients

source_name: MM_0170_B Bone marrow


title: MM_0167_B

description: Newly diagnosed patients

source_name: MM_0167_B Bone marrow


title: MM_0172_B

description: Newly diagnosed patients

source_name: MM_0172_B Bone marrow


title: MM_0166_B

description: Newly diagnosed patients

source_name: MM_0166_B Bone marrow


title: MM_0162_B

description: Newly diagnosed patients

source_name: MM_0162_B Bone marrow


title: MM_0163_B

description: Newly diagnosed patients

source_name: MM_0163_B Bone marrow


title: Thymol treated 1

source_name: Thymol treated 1

source_name: Saccharomyces cerevisiae_DMSO


title: MM_0159_B

description: Newly diagnosed patients

source_name: MM_0159_B Bone marrow


title: MM_0161_B

description: Newly diagnosed patients

source_name: MM_0161_B Bone marrow


title: MM_0160_B

description: Newly diagnosed patients

source_name: MM_0160_B Bone marrow


title: MM_0155_B

description: Newly diagnosed patients

source_name: MM_0155_B Bone marrow


title: MM_0157_B

description: Newly diagnosed patients

source_name: MM_0157_B Bone marrow


title: MM_0156_B

description: Newly diagnosed patients

source_name: MM_0156_B Bone marrow


title: MM_0154_B

description: Newly diagnosed patients

source_name: MM_0154_B Bone marrow


title: MM_0153_B

description: Newly diagnosed patients

source_name: MM_0153_B Bone marrow


title: MM_0148_B

description: Newly diagnosed patients

source_name: MM_0148_B Bone marrow


title: MM_0144_B

description: Newly diagnosed patients

source_name: MM_0144_B Bone marrow


title: MM_0152_B

description: Newly diagnosed patients

source_name: MM_0152_B Bone marrow


title: MM_0149_B

description: Newly diagnosed patients

source_name: MM_0149_B Bone marrow


title: MM_0146_B

description: Newly diagnosed patients

source_name: MM_0146_B Bone marrow


title: MM_0147_B

description: Newly diagnosed patients

source_name: MM_0147_B Bone marrow


title: MM_0150_B

description: Newly diagnosed patients

source_name: MM_0150_B Bone marrow


title: MM_0145_B

description: Newly diagnosed patients

source_name: MM_0145_B Bone marrow


title: MM_0165_B

description: Newly diagnosed patients

source_name: MM_0165_B Bone marrow


title: MM_0138_B

description: Newly diagnosed patients

source_name: MM_0138_B Bone marrow


title: MM_0139_B

description: Newly diagnosed patients

source_name: MM_0139_B Bone marrow


title: MM_0142_B

description: Newly diagnosed patients

source_name: MM_0142_B Bone marrow


title: MM_0143_B

description: Newly diagnosed patients

source_name: MM_0143_B Bone marrow


title: MM_0141_B

description: Newly diagnosed patients

source_name: MM_0141_B Bone marrow


title: MM_0137_B

description: Newly diagnosed patients

source_name: MM_0137_B Bone marrow


title: MM_0158_B

description: Newly diagnosed patients

source_name: MM_0158_B Bone marrow


title: MM_0164_B

description: Newly diagnosed patients

source_name: MM_0164_B Bone marrow


title: MM_0140_B

description: Newly diagnosed patients

source_name: MM_0140_B Bone marrow


title: MM_0136_B

description: Newly diagnosed patients

source_name: MM_0136_B Bone marrow


title: MM_0151_B

description: Newly diagnosed patients

source_name: MM_0151_B Bone marrow


title: MM_0134_B

description: Newly diagnosed patients

source_name: MM_0134_B Bone marrow


title: MM_0131_B

description: Newly diagnosed patients

source_name: MM_0131_B Bone marrow


title: MM_0132_B

description: Newly diagnosed patients

source_name: MM_0132_B Bone marrow


title: MM_0133_B

description: Newly diagnosed patients

source_name: MM_0133_B Bone marrow


title: MM_0130_B

description: Newly diagnosed patients

source_name: MM_0130_B Bone marrow


title: MM_0129_B

description: Newly diagnosed patients

source_name: MM_0129_B Bone marrow


title: MM_0127_B

description: Newly diagnosed patients

source_name: MM_0127_B Bone marrow


title: MM_0135_B

description: Newly diagnosed patients

source_name: MM_0135_B Bone marrow


title: MM_0128_B

description: Newly diagnosed patients

source_name: MM_0128_B Bone marrow


title: MM_0117_B

description: Newly diagnosed patients

source_name: MM_0117_B Bone marrow


title: MM_0126_B

description: Newly diagnosed patients

source_name: MM_0126_B Bone marrow


title: MM_0125_B

description: Newly diagnosed patients

source_name: MM_0125_B Bone marrow


title: MM_0124_B

description: Newly diagnosed patients

source_name: MM_0124_B Bone marrow


title: MM_0120_B

description: Newly diagnosed patients

source_name: MM_0120_B Bone marrow


title: MM_0123_B

description: Newly diagnosed patients

source_name: MM_0123_B Bone marrow


title: MM_0121_B

description: Newly diagnosed patients

source_name: MM_0121_B Bone marrow


title: MM_0112_B

description: Newly diagnosed patients

source_name: MM_0112_B Bone marrow


title: MM_0116_B

description: Newly diagnosed patients

source_name: MM_0116_B Bone marrow


title: MM_0119_B

description: Newly diagnosed patients

source_name: MM_0119_B Bone marrow


title: MM_0118_B

description: Newly diagnosed patients

source_name: MM_0118_B Bone marrow


title: MM_0113_B

description: Newly diagnosed patients

source_name: MM_0113_B Bone marrow


title: MM_0114_B

description: Newly diagnosed patients

source_name: MM_0114_B Bone marrow


title: MM_0111_B

description: Newly diagnosed patients

source_name: MM_0111_B Bone marrow


title: MM_0108_B

description: Newly diagnosed patients

source_name: MM_0108_B Bone marrow


title: MM_0109_B

description: Newly diagnosed patients

source_name: MM_0109_B Bone marrow


title: MM_0115_B

description: Newly diagnosed patients

source_name: MM_0115_B Bone marrow


title: MM_0110_B

description: Newly diagnosed patients

source_name: MM_0110_B Bone marrow


title: MM_0107_B

description: Newly diagnosed patients

source_name: MM_0107_B Bone marrow


title: MM_0122_B

description: Newly diagnosed patients

source_name: MM_0122_B Bone marrow


title: MM_0105_B

description: Newly diagnosed patients

source_name: MM_0105_B Bone marrow


title: MM_0101_B

description: Newly diagnosed patients

source_name: MM_0101_B Bone marrow


title: MM_0102_B

description: Newly diagnosed patients

source_name: MM_0102_B Bone marrow


title: MM_0098_B

description: Newly diagnosed patients

source_name: MM_0098_B Bone marrow


title: MM_0104_B

description: Newly diagnosed patients

source_name: MM_0104_B Bone marrow


title: MM_0103_B

description: Newly diagnosed patients

source_name: MM_0103_B Bone marrow


title: MM_0100_B

description: Newly diagnosed patients

source_name: MM_0100_B Bone marrow


title: MM_0096_B

description: Newly diagnosed patients

source_name: MM_0096_B Bone marrow


title: MM_0099_B

description: Newly diagnosed patients

source_name: MM_0099_B Bone marrow


title: MM_0094_B

description: Newly diagnosed patients

source_name: MM_0094_B Bone marrow


title: MM_0106_B

description: Newly diagnosed patients

source_name: MM_0106_B Bone marrow


title: MM_0090_B

description: Newly diagnosed patients

source_name: MM_0090_B Bone marrow


title: MM_0091_B

description: Newly diagnosed patients

source_name: MM_0091_B Bone marrow


title: MM_0089_B

description: Newly diagnosed patients

source_name: MM_0089_B Bone marrow


title: MM_0088_B

description: Newly diagnosed patients

source_name: MM_0088_B Bone marrow


title: MM_0086_B

description: Newly diagnosed patients

source_name: MM_0086_B Bone marrow


title: MM_0092_B

description: Newly diagnosed patients

source_name: MM_0092_B Bone marrow


title: MM_0084_B

description: Newly diagnosed patients

source_name: MM_0084_B Bone marrow


title: MM_0085_B

description: Newly diagnosed patients

source_name: MM_0085_B Bone marrow


title: MM_0087_B

description: Newly diagnosed patients

source_name: MM_0087_B Bone marrow


title: MM_0097_B

description: Newly diagnosed patients

source_name: MM_0097_B Bone marrow


title: MM_0082_B

description: Newly diagnosed patients

source_name: MM_0082_B Bone marrow


title: MM_0081_B

description: Newly diagnosed patients

source_name: MM_0081_B Bone marrow


title: MM_0095_B

description: Newly diagnosed patients

source_name: MM_0095_B Bone marrow


title: MM_0080_B

description: Newly diagnosed patients

source_name: MM_0080_B Bone marrow


title: MM_0083_B

description: Newly diagnosed patients

source_name: MM_0083_B Bone marrow


title: MM_0078_B

description: Newly diagnosed patients

source_name: MM_0078_B Bone marrow


title: MM_0093_B

description: Newly diagnosed patients

source_name: MM_0093_B Bone marrow


title: MM_0079_B

description: Newly diagnosed patients

source_name: MM_0079_B Bone marrow


title: MM_0072_B

description: Newly diagnosed patients

source_name: MM_0072_B Bone marrow


title: MM_0073_B

description: Newly diagnosed patients

source_name: MM_0073_B Bone marrow


title: MM_0069_B

description: Newly diagnosed patients

source_name: MM_0069_B Bone marrow


title: MM_0077_B

description: Newly diagnosed patients

source_name: MM_0077_B Bone marrow


title: MM_0076_B

description: Newly diagnosed patients

source_name: MM_0076_B Bone marrow


title: MM_0071_B

description: Newly diagnosed patients

source_name: MM_0071_B Bone marrow


title: MM_0068_B

description: Newly diagnosed patients

source_name: MM_0068_B Bone marrow


title: MM_0065_B

description: Newly diagnosed patients

source_name: MM_0065_B Bone marrow


title: MM_0066_B

description: Newly diagnosed patients

source_name: MM_0066_B Bone marrow


title: MM_0067_B

description: Newly diagnosed patients

source_name: MM_0067_B Bone marrow


title: MM_0062_B

description: Newly diagnosed patients

source_name: MM_0062_B Bone marrow


title: MM_0063_B

description: Newly diagnosed patients

source_name: MM_0063_B Bone marrow


title: MM_0060_B

description: Newly diagnosed patients

source_name: MM_0060_B Bone marrow


title: MM_0074_B

description: Newly diagnosed patients

source_name: MM_0074_B Bone marrow


title: MM_0059_B

description: Newly diagnosed patients

source_name: MM_0059_B Bone marrow


title: MM_0075_B

description: Newly diagnosed patients

source_name: MM_0075_B Bone marrow


title: MM_0058_B

description: Newly diagnosed patients

source_name: MM_0058_B Bone marrow


title: MM_0057_B

description: Newly diagnosed patients

source_name: MM_0057_B Bone marrow


title: MM_0054_B

description: Newly diagnosed patients

source_name: MM_0054_B Bone marrow


title: MM_0055_B

description: Newly diagnosed patients

source_name: MM_0055_B Bone marrow


title: MM_0053_B

description: Newly diagnosed patients

source_name: MM_0053_B Bone marrow


title: MM_0056_B

description: Newly diagnosed patients

source_name: MM_0056_B Bone marrow


title: MM_0051_B

description: Newly diagnosed patients

source_name: MM_0051_B Bone marrow


title: MM_0064_B

description: Newly diagnosed patients

source_name: MM_0064_B Bone marrow


title: MM_0050_B

description: Newly diagnosed patients

source_name: MM_0050_B Bone marrow


title: MM_0049_B

description: Newly diagnosed patients

source_name: MM_0049_B Bone marrow


title: MM_0048_B

description: Newly diagnosed patients

source_name: MM_0048_B Bone marrow


title: MM_0047_B

description: Newly diagnosed patients

source_name: MM_0047_B Bone marrow


title: MM_0046_B

description: Newly diagnosed patients

source_name: MM_0046_B Bone marrow


title: MM_0045_B

description: Newly diagnosed patients

source_name: MM_0045_B Bone marrow


title: MM_0061_B

description: Newly diagnosed patients

source_name: MM_0061_B Bone marrow


title: MM_0044_B

description: Newly diagnosed patients

source_name: MM_0044_B Bone marrow


title: MM_0038_B

description: Newly diagnosed patients

source_name: MM_0038_B Bone marrow


title: MM_0041_B

description: Newly diagnosed patients

source_name: MM_0041_B Bone marrow


title: MM_0042_B

description: Newly diagnosed patients

source_name: MM_0042_B Bone marrow


title: MM_0039_B

description: Newly diagnosed patients

source_name: MM_0039_B Bone marrow


title: MM_0052_B

description: Newly diagnosed patients

source_name: MM_0052_B Bone marrow


title: MM_0036_B

description: Newly diagnosed patients

source_name: MM_0036_B Bone marrow


title: MM_0040_B

description: Newly diagnosed patients

source_name: MM_0040_B Bone marrow


title: MM_0034_B

description: Newly diagnosed patients

source_name: MM_0034_B Bone marrow


title: MM_0035_B

description: Newly diagnosed patients

source_name: MM_0035_B Bone marrow


title: MM_0037_B

description: Newly diagnosed patients

source_name: MM_0037_B Bone marrow


title: MM_0043_B

description: Newly diagnosed patients

source_name: MM_0043_B Bone marrow


title: MM_0033_B

description: Newly diagnosed patients

source_name: MM_0033_B Bone marrow


title: MM_0070_B

description: Newly diagnosed patients

source_name: MM_0070_B Bone marrow


title: MM_0031_B

description: Newly diagnosed patients

source_name: MM_0031_B Bone marrow


title: MM_0028_B

description: Newly diagnosed patients

source_name: MM_0028_B Bone marrow


title: MM_0032_B

description: Newly diagnosed patients

source_name: MM_0032_B Bone marrow


title: MM_0030_B

description: Newly diagnosed patients

source_name: MM_0030_B Bone marrow


title: MM_0029_B

description: Newly diagnosed patients

source_name: MM_0029_B Bone marrow


title: MM_0027_B

description: Newly diagnosed patients

source_name: MM_0027_B Bone marrow


title: MM_0025_B

description: Newly diagnosed patients

source_name: MM_0025_B Bone marrow


title: MM_0026_B

description: Newly diagnosed patients

source_name: MM_0026_B Bone marrow


title: MM_0023_B

description: Newly diagnosed patients

source_name: MM_0023_B Bone marrow


title: MM_0024_B

description: Newly diagnosed patients

source_name: MM_0024_B Bone marrow


title: brain_young_PPB_2

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description:
348_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on PPB diet

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine Genome Array (version 1) using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages. Additionally, Affymetrix's Call Detection algorithm was used to exclude probesets that were not called Present on at least one array or Marginal on two arrays from differential analysis.

organism: Canis lupus familiaris

source_name: Cerebral cortex at 1 yr, after 1 year on PPB diet

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Young dogs (mean age = 8 wk at baseline) were fed ad libitum throughout the study to allow for adequate growth; old dogs (mean age = 11.1 yr at baseline) were fed to maintain baseline BW.

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were allotted to 1 of 2 diets and fed for 12 months: 1) animal-protein based (APB) diet primarily composed of highly digestible, animal-derived ingredients and formulated to exceed protein and fat recommendations provided by the Association of American Feed Control Officials (AAFCO) for growth and reproduction; or 2) plant-protein based (PPB) diet primarily composed of moderately digestible, plant-derived ingredients and formulated to meet protein and fat recommendations for growth and reproduction by AAFCO.  The exception was 10% meat and bone meal in the diet.  All samples were collected after an overnight food-restricted period.

value: Brain; cerebral cortex

tag: Age

value: 1 yr

tag: Diet

value: Plant-Protein Based

tag: Breed

value: Beagle


title: brain_young_APB_1

description:
345_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on APB diet

source_name: Cerebral cortex at 1 yr, after 1 year on APB diet

value: Animal-Protein Based


title: brain_young_PPB_1

description:
346_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on PPB diet


title: Transection day 37 lesion

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

hyb_protocol: The fragmented cRNA sample was hybridized to Affymetrix rat U34A microarray for 16 hours at 60rpm at 45Â°C. The microarrays were then washed and stained on the Affymetrix Fluidics Station 400 using instructions and reagents purchased from Affymetrix.

scan_protocol: Scanning was performed with a Hewlett-Packard G2500A Gene Array Scanner.

data_processing: Probe-level summarization was accomplished using the Affymetrix MAS 5.0 Algorithm. Resulting expression data was log (base=2) transformed and quantile normalized using R (bioconductor). Expression data construed as noise by Affymetrix Control Fragment modeling (Coeficient of Variation ~ expression) were floored to 6.35. While, four additional expression measurements for each gene fragment for each corresponding microarray were created using the model in conjunction with the random normal distribution. Per gene fragment selection, analysis of variance (i.e., ANOVA) was used in conjunction with a minimum effect difference filter. Such that, gene fragments having a Bonferroni family-wise error multiple comparison corrected p-value < 0.05 and a 2-fold minimum effect difference were kept for use in Temporal clustering analysis.

organism: Rattus norvegicus

source_name: pontine nuclei transection day37 lesion

label_protocol: Seven micrograms from each total RNA sample was converted into double-stranded cDNA by using SuperScript choice system with an oligo-dT primer containing T7 RNA polymerase promoter. The double-stranded cDNA was purified by phenol/chloroform extraction and then used for in vitro transcription using ENZO BioArray RNA transcript labelling kit.  Biotin-labelled cRNA was purified with the RNeasy kit and fragmented to approximately 200bp.

extract_protocol: Trizol reagent

tag: adult male Sprague-Dawley rats


title: MM_0022_B

description: Newly diagnosed patients

source_name: MM_0022_B Bone marrow


title: brain_old_PPB_3

description:
344R_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on PPB diet

source_name: Cerebral cortex at 12 yrs, after 1 year on PPB diet

value: 12 yrs


title: brain_young_APB_2

description:
347_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on APB diet


title: brain_old_PPB_2

description:
342_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on PPB diet


title: brain_young_APB_3

description:
349_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on APB diet


title: brain_old_APB_3

description:
343_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on APB diet

source_name: Cerebral cortex at 12 yrs, after 1 year on APB diet


title: brain_young_PPB_3

description:
350_E.CEL
Gene expression data from cerebral cortex of 1 yr-old dogs after 1 yr on PPB diet